1
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Hu T, Xuan R, Han E, Cai L, Xia Z. SPOPL induces tumorigenicity and stemness in glioma stem cells by activating Notch signaling. J Neurooncol 2023; 164:157-170. [PMID: 37523046 DOI: 10.1007/s11060-023-04394-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVE Recent studies have increasingly shown that glioma stem cells (GSCs) are extremely important for developing and treating glioblastoma multiforme (GBM). The Broad-complex, Tram-track, and Bric-a-brac protein family is functionally related to a variety of tumor stem cells, and the role of SPOPL as a member of this family in GSCs deserves to be investigated. METHODS To investigate the expression of SPOPL in GSCs and its impact on the prognosis of GBM patients by using clinical specimens, patient-derived primary GSCs and public databases. In vivo and in vitro, the effect of SPOPL on the proliferation, self-renewal, and differentiation ability of GSCs was explored. Probing the mechanism by which SPOPL affects the biological function of GSCs using RNA sequencing (RNA-seq) and rescue experiments. RESULTS The expression of SPOPL was significantly upregulated in GSCs and GBM, and patients with high SPOPL expression had a poorer prognosis. SPOPL enhanced the proliferation and self-renewal ability of GSCs and enhanced the tumorigenicity of GSCs. The Notch signaling pathway was significantly inhibited in SPOPL knockdown GSCs. Activation or inhibition of the Notch signaling pathway rescued changes in the biological function of GSCs caused by altered SPOPL expression. CONCLUSION SPOPL can be used as a potential prognostic biomarker for GBM in clinical work and promotes the proliferation and stemness of GSCs by activating the Notch signaling pathway, which may be a potential molecule for targeting GSCs to treat GBM.
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Affiliation(s)
- Tianyu Hu
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ruoheng Xuan
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Erqiao Han
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingshan Cai
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhibo Xia
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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2
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Mutsuddy A, Erdem C, Huggins JR, Salim M, Cook D, Hobbs N, Feltus FA, Birtwistle MR. Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format. BIOINFORMATICS ADVANCES 2023; 3:vbad039. [PMID: 37020976 PMCID: PMC10070034 DOI: 10.1093/bioadv/vbad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/25/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023]
Abstract
Summary Large-scale and whole-cell modeling has multiple challenges, including scalable model building and module communication bottlenecks (e.g. between metabolism, gene expression, signaling, etc.). We previously developed an open-source, scalable format for a large-scale mechanistic model of proliferation and death signaling dynamics, but communication bottlenecks between gene expression and protein biochemistry modules remained. Here, we developed two solutions to communication bottlenecks that speed-up simulation by ∼4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations. Fully deterministic speed-up facilitates model initialization, parameter estimation and sensitivity analysis tasks. Availability and implementation Source code is freely available at https://github.com/birtwistlelab/SPARCED/releases/tag/v1.3.0 implemented in python, and supported on Linux, Windows and MacOS (via Docker).
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Affiliation(s)
- Arnab Mutsuddy
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Cemal Erdem
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Jonah R Huggins
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
- School of Computing, Clemson University, Clemson, SC, USA
| | | | | | | | - F Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
- Department of Bioengineering, Clemson University, Clemson, SC, USA
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3
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Martins dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Dominguez Del Angel V, Domínguez-Romero E, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, T. Scott W, Sheriff RSM, Suarez Diez M, Van Steen K, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM. Systems Biology in ELIXIR: modelling in the spotlight. F1000Res 2022; 11:ELIXIR-1265. [PMID: 36742342 PMCID: PMC9871403 DOI: 10.12688/f1000research.126734.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
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Affiliation(s)
- Vitor Martins dos Santos
- Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Mihail Anton
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258, Sweden
| | - Barbara Szomolay
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Ilja Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | | | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4, Ireland
| | - Carole Goble
- Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
| | | | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Maria I. Klapa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
| | - Jasper Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
| | - Alexey Kolodkin
- Competence Center for Methodology and Statistics; Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445, Luxembourg
- ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | | | - Wolfgang Müller
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Marco Pagni
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tadeja Rezen
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Damjana Rozman
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - David Šafránek
- Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
- UNLOCK, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Rahuman S. Malik Sheriff
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Suarez Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
| | - Kristel Van Steen
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, 4000, Belgium
| | | | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Katherine Wolstencroft
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA, The Netherlands
| | - Anze Zupanic
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - John M. Hancock
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
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4
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Martins dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Dominguez Del Angel V, Domínguez-Romero E, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, T. Scott W, Sheriff RSM, Suarez Diez M, Van Steen K, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM. Systems Biology in ELIXIR: modelling in the spotlight. F1000Res 2022; 11:ELIXIR-1265. [PMID: 36742342 PMCID: PMC9871403 DOI: 10.12688/f1000research.126734.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
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Affiliation(s)
- Vitor Martins dos Santos
- Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Mihail Anton
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258, Sweden
| | - Barbara Szomolay
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Ilja Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | | | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4, Ireland
| | - Carole Goble
- Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
| | | | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Maria I. Klapa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
| | - Jasper Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
| | - Alexey Kolodkin
- Competence Center for Methodology and Statistics; Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445, Luxembourg
- ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | | | - Wolfgang Müller
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Marco Pagni
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tadeja Rezen
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Damjana Rozman
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
| | - David Šafránek
- Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
- UNLOCK, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Rahuman S. Malik Sheriff
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Suarez Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
| | - Kristel Van Steen
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, 4000, Belgium
| | | | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
| | - Katherine Wolstencroft
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA, The Netherlands
| | - Anze Zupanic
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - John M. Hancock
- Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
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5
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Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR. A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nat Commun 2022; 13:3555. [PMID: 35729113 PMCID: PMC9213456 DOI: 10.1038/s41467-022-31138-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFNγ pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFNγ acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFNγ-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.
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Affiliation(s)
- Cemal Erdem
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC, USA.
| | - Arnab Mutsuddy
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Ethan M Bensman
- Computer Science, School of Computing, Clemson University, Clemson, SC, USA
| | - William B Dodd
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Michael M Saint-Antoine
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robert C Blake
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Sean M Gross
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - F Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Clemson, SC, USA
| | - Marc R Birtwistle
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC, USA.
- Department of Bioengineering, Clemson University, Clemson, SC, USA.
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6
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Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Rueda OM, Charmpi K, Esmaeilishirazifard E, Bruna A, de Souza N, Caldas C, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Syst 2021; 12:401-418.e12. [PMID: 33932331 DOI: 10.1016/j.cels.2021.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 12/16/2020] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
One goal of precision medicine is to tailor effective treatments to patients' specific molecular markers of disease. Here, we used mass cytometry to characterize the single-cell signaling landscapes of 62 breast cancer cell lines and five lines from healthy tissue. We quantified 34 markers in each cell line upon stimulation by the growth factor EGF in the presence or absence of five kinase inhibitors. These data-on more than 80 million single cells from 4,000 conditions-were used to fit mechanistic signaling network models that provide insight into how cancer cells process information. Our dynamic single-cell-based models accurately predicted drug sensitivity and identified genomic features associated with drug sensitivity, including a missense mutation in DDIT3 predictive of PI3K-inhibition sensitivity. We observed similar trends in genotype-drug sensitivity associations in patient-derived xenograft mouse models. This work provides proof of principle that patient-specific single-cell measurements and modeling could inform effective precision medicine strategies.
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Affiliation(s)
- Marco Tognetti
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland; Molecular Life Science PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8057 Zurich, Switzerland
| | - Attila Gabor
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69117 Heidelberg, Germany; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Mi Yang
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany
| | | | - Jonas Windhager
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland; Systems Biology PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8093 Zürich, Switzerland
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Konstantina Charmpi
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), Medical Faculty and Faculty of Mathematics and Natural Sciences, University of Cologne, 50923 Cologne, Germany
| | - Elham Esmaeilishirazifard
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Bioscience, R&D Oncology, Astra Zeneca, Cancer Research UK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Alejandra Bruna
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Cambridge Breast Unit, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre at Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), Medical Faculty and Faculty of Mathematics and Natural Sciences, University of Cologne, 50923 Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50923 Cologne, Germany; Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50923 Cologne, Germany
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69117 Heidelberg, Germany; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland.
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7
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Khalafallah AM, Huq S, Jimenez AE, Serra R, Bettegowda C, Mukherjee D. "Zooming in" on Glioblastoma: Understanding Tumor Heterogeneity and its Clinical Implications in the Era of Single-Cell Ribonucleic Acid Sequencing. Neurosurgery 2021; 88:477-486. [PMID: 32674143 DOI: 10.1093/neuros/nyaa305] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary brain malignancy in adults and one of the most aggressive of all human cancers. It is highly recurrent and treatment-resistant, in large part due to its infiltrative nature and inter- and intratumoral heterogeneity. This heterogeneity entails varying genomic landscapes and cell types within and between tumors and the tumor microenvironment (TME). In GBM, heterogeneity is a driver of treatment resistance, recurrence, and poor prognosis, representing a substantial impediment to personalized medicine. Over the last decade, sequencing technologies have facilitated deeper understanding of GBM heterogeneity by "zooming in" progressively further on tumor genomics and transcriptomics. Initial efforts employed bulk ribonucleic acid (RNA) sequencing, which examines composite gene expression of whole tumor specimens. While groundbreaking at the time, this bulk RNAseq masks the crucial contributions of distinct tumor subpopulations to overall gene expression. This work progressed to the use of bulk RNA sequencing in anatomically and spatially distinct tumor subsections, which demonstrated previously underappreciated genomic complexity of GBM. A revolutionary next step forward has been the advent of single-cell RNA sequencing (scRNAseq), which examines gene expression at the single-cell level. scRNAseq has enabled us to understand GBM heterogeneity in unprecedented detail. We review seminal studies in our progression of understanding GBM heterogeneity, with a focus on scRNAseq and the insights that it has provided into understanding the GBM tumor mass, peritumoral space, and TME. We highlight preclinical and clinical implications of this work and consider its potential to impact neuro-oncology and to improve patient outcomes via personalized medicine.
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Affiliation(s)
| | | | - Adrian E Jimenez
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Riccardo Serra
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Debraj Mukherjee
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
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8
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Bhalerao A, Sivandzade F, Archie SR, Chowdhury EA, Noorani B, Cucullo L. In vitro modeling of the neurovascular unit: advances in the field. Fluids Barriers CNS 2020; 17:22. [PMID: 32178700 PMCID: PMC7077137 DOI: 10.1186/s12987-020-00183-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
The blood–brain barrier (BBB) is a fundamental component of the central nervous system. Its functional and structural integrity is vital in maintaining the homeostasis of the brain microenvironment. On the other hand, the BBB is also a major hindering obstacle for the delivery of effective therapies to treat disorders of the Central Nervous System (CNS). Over time, various model systems have been established to simulate the complexities of the BBB. The development of realistic in vitro BBB models that accurately mimic the physiological characteristics of the brain microcapillaries in situ is of fundamental importance not only in CNS drug discovery but also in translational research. Successful modeling of the Neurovascular Unit (NVU) would provide an invaluable tool that would aid in dissecting out the pathological factors, mechanisms of action, and corresponding targets prodromal to the onset of CNS disorders. The field of BBB in vitro modeling has seen many fundamental changes in the last few years with the introduction of novel tools and methods to improve existing models and enable new ones. The development of CNS organoids, organ-on-chip, spheroids, 3D printed microfluidics, and other innovative technologies have the potential to advance the field of BBB and NVU modeling. Therefore, in this review, summarize the advances and progress in the design and application of functional in vitro BBB platforms with a focus on rapidly advancing technologies.
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Affiliation(s)
- Aditya Bhalerao
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Farzane Sivandzade
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Sabrina Rahman Archie
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Ekram Ahmed Chowdhury
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Behnam Noorani
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Luca Cucullo
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA. .,Center for Blood-Brain Barrier Research, Texas Tech University Health Sciences Center, Amarillo, TX, 79106, USA.
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9
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Abstract
Dynamic mechanistic models, that is, those that can simulate behavior over time courses, are a cornerstone of molecular systems biology. They are being used to model molecular mechanisms with varying degrees of granularity-from elementary reactions to causal links-and to describe these systems by various dynamic mathematical frameworks, such as Boolean networks or systems of differential equations. The models can be based exclusively on experimental data, or on prior knowledge of the underlying biological processes. The latter are typically generic, but can be adapted to a certain context, such as a particular cell type, after training with context-specific data. Dynamic mechanistic models that are based on biological knowledge have great potential for modeling specific systems, because they require less data for training to provide biological insight in particular into causal mechanisms, and to extrapolate to scenarios that are outside the conditions they have been trained on.
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Affiliation(s)
- Julio Saez‐Rodriguez
- Faculty of MedicineHeidelberg University and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
| | - Nils Blüthgen
- Institute of PathologyCharité ‐ Universitätsmedizin BerlinBerlinGermany
- IRI Life SciencesHumboldt Universität zu BerlinBerlinGermany
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10
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Fan S, Gao H, Ji W, Zhu F, Sun L, Liu Y, Zhang S, Xu Y, Yan Y, Gao Y. Umbilical cord-derived mesenchymal stromal/stem cells expressing IL-24 induce apoptosis in gliomas. J Cell Physiol 2019; 235:1769-1779. [PMID: 31301067 DOI: 10.1002/jcp.29095] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
Abstract
Although much progress has been made in the treatment of gliomas, the prognosis for patients with gliomas is still very poor. Stem cell-based therapies may be promising options for glioma treatment. Recently, many studies have reported that umbilical cord-derived mesenchymal stromal/stem cells (UC-MSCs) are ideal gene vehicles for tumor gene therapy. Interleukin 24 (IL-24) is a pleiotropic immunoregulatory cytokine that has an apoptotic effect on many kinds of tumor cells and can inhibit the growth of tumors specifically without damaging normal cells. In this study, we investigated UC-MSCs as a vehicle for the targeted delivery of IL-24 to tumor sites. UC-MSCs were transduced with lentiviral vectors carrying green fluorescent protein (GFP) or IL-24 complementary DNA. The results indicated that UC-MSCs could selectively migrate to glioma cells in vitro and in vivo. Injection of IL-24-UC-MSCs significantly suppressed tumor growth of glioma xenografts. The restrictive efficacy of IL-24-UC-MSCs was associated with the inhibition of proliferation as well as the induction of apoptosis in tumor cells. These findings indicate that UC-MSC-based IL-24 gene therapy may be able to suppress the growth of glioma xenografts, thereby suggesting possible future therapeutic use in the treatment of gliomas.
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Affiliation(s)
- Shaochen Fan
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Huasong Gao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Ji
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Fengwei Zhu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Lingzheng Sun
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuankun Liu
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Siming Zhang
- Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Yanran Xu
- Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Yaohua Yan
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yilu Gao
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
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11
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Jackson S, Meeks C, Vézina A, Robey RW, Tanner K, Gottesman MM. Model systems for studying the blood-brain barrier: Applications and challenges. Biomaterials 2019; 214:119217. [PMID: 31146177 DOI: 10.1016/j.biomaterials.2019.05.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 12/21/2022]
Abstract
The blood-brain barrier (BBB) poses a serious impediment to the delivery of effective therapies to the central nervous system (CNS). Over time, various model systems have been crafted and used to evaluate the complexities of the BBB, which includes an impermeable physical barrier and a series of energy-dependent efflux pumps. Models of the BBB have mainly sought to assess changes in endothelial cell permeability, the role of ATP-dependent efflux transporters in drug disposition, and alterations in communication between BBB cells and the microenvironment. In the context of disease, various animal models have been utilized to examine real time BBB drug permeability, CNS dynamic changes, and overall treatment response. In this review, we outline the use of these in vitro and in vivo blood-brain barrier model systems to study normal physiology and diseased states. These current models each have their own advantages and disadvantages for studying the response of biologic processes to physiological and pathological conditions. Additional models are needed to mimic more closely the dynamic quality of the BBB, with the goal focused on potential clinical applications.
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Affiliation(s)
- Sadhana Jackson
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
| | - Caitlin Meeks
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Amélie Vézina
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Robert W Robey
- Multidrug Resistance Section, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Kandice Tanner
- Tissue Morphodynamics Unit, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Michael M Gottesman
- Multidrug Resistance Section, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
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12
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van Hasselt JGC, Iyengar R. Systems Pharmacology: Defining the Interactions of Drug Combinations. Annu Rev Pharmacol Toxicol 2018; 59:21-40. [PMID: 30260737 DOI: 10.1146/annurev-pharmtox-010818-021511] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The majority of diseases are associated with alterations in multiple molecular pathways and complex interactions at the cellular and organ levels. Single-target monotherapies therefore have intrinsic limitations with respect to their maximum therapeutic benefits. The potential of combination drug therapies has received interest for the treatment of many diseases and is well established in some areas, such as oncology. Combination drug treatments may allow us to identify synergistic drug effects, reduce adverse drug reactions, and address variability in disease characteristics between patients. Identification of combination therapies remains challenging. We discuss current state-of-the-art systems pharmacology approaches to enable rational identification of combination therapies. These approaches, which include characterization of mechanisms of disease and drug action at a systems level, can enable understanding of drug interactions at the molecular, cellular, physiological, and organismal levels. Such multiscale understanding can enable precision medicine by promoting the rational development of combination therapy at the level of individual patients for many diseases.
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Affiliation(s)
- J G Coen van Hasselt
- Department of Pharmacological Sciences, Systems Biology Center, Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, 2333 Leiden, Netherlands;
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Systems Biology Center, Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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Li SC, Kabeer MH. Spatiotemporal switching signals for cancer stem cell activation in pediatric origins of adulthood cancer: Towards a watch-and-wait lifetime strategy for cancer treatment. World J Stem Cells 2018; 10:15-22. [PMID: 29531638 PMCID: PMC5840533 DOI: 10.4252/wjsc.v10.i2.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 02/06/2023] Open
Abstract
Pediatric origin of cancer stem cell hypothesis holds great promise and potential in adult cancer treatment, however; the road to innovation is full of obstacles as there are plenty of questions left unanswered. First, the key question is to characterize the nature of such stem cells (concept). Second, the quantitative imaging of pediatric stem cells should be implemented (technology). Conceptually, pediatric stem cell origins of adult cancer are based on the notion that plasticity in early life developmental programming evolves local environments to cancer. Technologically, such imaging in children is lacking as all imaging is designed for adult patients. We postulate that the need for quantitative imaging to measure space-time changes of plasticity in early life developmental programming in children may trigger research and development of the imaging technology. Such quantitative imaging of pediatric origin of adulthood cancer will help develop a spatiotemporal monitoring system to determine cancer initiation and progression. Clinical validation of such speculative hypothesis-that cancer originates in a pediatric environment-will help implement a wait-and-watch strategy for cancer treatment.
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Affiliation(s)
- Shengwen Calvin Li
- Neuro-oncology and Stem Cell Research Laboratory, Children’s Hospital of Orange County, Department of Neurology, University of California-Irvine School of Medicine, Orange, CA 92868-3874, United States
| | - Mustafa H Kabeer
- Children's Hospital of Orange County, Department of Surgery, University of California-Irvine School of Medicine, Orange, CA 92868-3874, United States
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14
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Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma. PLoS One 2018; 13:e0190664. [PMID: 29342193 PMCID: PMC5771580 DOI: 10.1371/journal.pone.0190664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Current treatments for glioblastoma multiforme (GBM)-an aggressive form of brain cancer-are minimally effective and yield a median survival of 14.6 months and a two-year survival rate of 30%. Given the severity of GBM and the limitations of its treatment, there is a need for the discovery of novel drug targets for GBM and more personalized treatment approaches based on the characteristics of an individual's tumor. Most receptor tyrosine kinases-such as EGFR-act as oncogenes, but publicly available data from the Cancer Cell Line Encyclopedia (CCLE) indicates copy number loss in the ERBB4 RTK gene across dozens of GBM cell lines, suggesting a potential tumor suppressor role. This loss is mutually exclusive with loss of its cognate ligand NRG1 in CCLE as well, more strongly suggesting a functional role. The availability of higher resolution copy number data from clinical GBM patients in The Cancer Genome Atlas (TCGA) revealed that a region in Intron 1 of the ERBB4 gene was deleted in 69.1% of tumor samples harboring ERBB4 copy number loss; however, it was also found to be deleted in the matched normal tissue samples from these GBM patients (n = 81). Using the DECIPHER Genome Browser, we also discovered that this mutation occurs at approximately the same frequency in the general population as it does in the disease population. We conclude from these results that this loss in Intron 1 of the ERBB4 gene is neither a de novo driver mutation nor a predisposing factor to GBM, despite the indications from CCLE. A biological role of this significantly occurring genetic alteration is still unknown. While this is a negative result, the broader conclusion is that while copy number data from large cell line-based data repositories may yield compelling hypotheses, careful follow up with higher resolution copy number assays, patient data, and general population analyses are essential to codify initial hypotheses prior to investing experimental resources.
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